Pharmaceutical Compositions for High-Capacity Targeted Delivery

ABSTRACT

Provided herein are aptamers and pharmaceutical compositions comprising the same. In some embodiments, the aptamer selectively binds a protein of interest such as an extracellular receptor protein of interest (e.g., a cancer cell extracellular receptor protein, which may be differentially expressed in some embodiments). In some embodiments, the aptamer is directly linked by covalent bonding (e.g., via a geminal diamine linkage) to from 2 to 10 toxin compounds. Also provided herein is a method of selecting an aptamer that specifically binds to a protein expressed by a cell of interest, wherein in some embodiments the aptamer comprises at least one binding site for one or more active compounds. In some embodiments, primer regions flanking the variable region of the aptamers in the pool contains from 1 to 10 mismatches with respect to said forward or reverse primer.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application SerialNo. 6¹/₈83,270, filed Sep. 27, 2013, the disclosure of which isincorporated by reference herein in its entirety.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grants DOD PCRP093606 and NIH-NCI P30CA012197. The government has certain rights inthis invention.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, submitted under 37 C.F.R. §1.821, entitled 9151-197_ST25.txt, 2,003 bytes in size, generated onSep. 25, 2014, and filed via EFS-Web, is provided in lieu of a papercopy. This Sequence Listing is hereby incorporated by reference into thespecification for its disclosures.

BACKGROUND

Cell-specific delivery of cytotoxic drugs via passive and activetargeting is an important objective in order to improve cancerchemotherapy. Successful targeting may be accomplished if the targetingvehicle has appropriate dimensions for tumor localization via theenhanced permeability and retention (EPR) effect, and binds with highaffinity to an antigen that is specifically expressed by targeted cells.The drug complex should also be stable, such that the drug is retainedin the complex during targeting, which may take several hours, butreleased from the complex after binding to the targeted cell. Drugdelivery should also be efficient, releasing multiple drugs for eachsuccessfully targeted complex. There remains a need for new targeteddrug delivery approaches that display stability with high payloaddelivery in order to accomplish these goals.

BRIEF SUMMARY OF EMBODIMENTS

Provided herein are aptamers and pharmaceutical compositions comprisingthe same. In some embodiments, the aptamer selectively binds a proteinof interest such as an extracellular receptor protein of interest (e.g.,a cancer cell extracellular receptor protein, which may bedifferentially expressed in some embodiments). In some embodiments, theaptamer is directly linked by covalent bonding (e.g., via a geminaldiamine linkage) to from 2 to 10 toxin compounds.

In some embodiments, at least one of said toxin compounds is ananthracycline (e.g., doxorubicin, daunorubicin, etc.) or a taxane havinga free amine (e.g., paclitaxel, docetaxel, etc.). In some embodiments,the aptamer is directly linked by covalent bonding to said anthracyclineor said taxane at a CpG binding site on said aptamer.

In some embodiments, the half life of covalent bonding to the toxincompounds is at least 5 hours, e.g., in human blood plasma or otherbodily fluids and/or tissues.

In some embodiments, the aptamer comprises at least one FdUMP.

In some embodiments, the aptamer is provided as a dimeric complex. Insome embodiments, the cancer cell extracellular receptor protein is adimeric protein and said dimeric complex comprises a first nucleic acidthat selectively binds to said cancer cell extracellular receptorprotein, a second nucleic acid that also selectively binds to saidcancer cell extracellular receptor protein, and a linker connecting saidfirst and second nucleic acids. In some embodiments, the dimeric proteinis prostate specific membrane antigen (PSMA), transferrin receptor,carbonic anhydrase XII, or an ErbB receptor. In some embodiments, thelinker is double-stranded poly-DNA. In some embodiments, thedouble-stranded poly-DNA comprises at least one CpG binding site.

Also provided herein is a method of selecting an aptamer as describedherein that specifically binds to a protein expressed by a cell ofinterest, wherein in some embodiments the aptamer comprises at least onebinding site for one or more active compounds. In some embodiments,primer regions flanking the variable region of the aptamers in the poolcontains 1 to 10 mismatches with respect to said forward or reverseprimer. In some embodiments, the aptamer so selected has a shorterlength than the nucleic acids of said first pool as a result of primingat sites other than the primer regions during amplification (which sitesmay or may not overlap with the primer region(s), as would be understoodby one of skill in the art).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the secondary structure of a dimeric aptamer complexcontaining CpG sequences appended to the ends of the dA16 (SEQ ID NO:7)or T16 (SEQ ID NO:8), which anneal to form a linker. Boxes indicatepotential doxorubicin binding sites.

FIG. 2 presents a physical characterization of DAC and DAC-D. (a) Themelting temperature (Tm) of DAC and DAC-D was determined by measuringthe ultraviolet absorbance at 260 nm and by heating the samples at 0.7°C./minute. (b) Dox fluorescence was measured by exciting the sample witha 532 nm laser and reading the emission at 580 nm. The calculatedhalf-life of transfer from DAC-D was found to be 8.27 hours. Error barsrepresent mean±SD. DAC, dimeric aptamer complex; DAC-D, dimeric aptamercomplex with doxorubicin.

FIG. 3 presents flow cytometry data. Cells were incubated with DAC fortwo hours before measuring the amount of fluorescence emitted by eitherQuasar 670 or Quasar 570 as a readout for aptamer internalization.

FIG. 4 presents the results of treatment of cell cultures with thedimeric toxin-loaded construct, DAC-D. PC3 and C4-2 cells were incubatedalone or in coculture and were treated with DAC-D, DAC+Dox, or free-Doxfor 24 hours. Media was replaced and cells were allowed to grow for 48hours before determining viability. Percentage of Dox retained was foundby comparing the viability of DAC-D (or DAC+Dox) with Dox. There is nostatistical difference between C4-2 cells alone versus C4-2 cells incoculture, however there is a significant reduction in cytotoxicity forPC3 cells in coculture versus PC3 cells alone (P<0.05). Error barsrepresent mean±SEM. DAC, dimeric aptamer complex; DAC-D, dimeric aptamercomplex with doxorubicin; Dox, doxorubicin.

DETAILED DESCRIPTION OF EMBODIMENTS

The present invention is explained in greater detail below. All patentreferences cited herein are specifically incorporated by reference tothe extent they are consistent with the present disclosure. As used inthe description of the invention and the appended claims, the singularforms “a”, “an” and “the” are intended to include the plural forms aswell, unless the context clearly indicates otherwise. Furthermore, theterm “about,” as used herein when referring to a measurable value suchas an amount of a compound, dose, time, temperature, and the like, ismeant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1% ofthe specified amount. Also, as used herein, “and/or” refers to andencompasses any and all possible combinations of one or more of theassociated listed items, as well as the lack of combinations wheninterpreted in the alternative (“or”).

“Active compound” as used herein includes, but is not limited to, atoxin or cytotoxic agent such as a cytotoxic nucleoside or nucleotide.Other toxins or cytotoxic agents useful as active compounds in thepresent invention include, but are not limited to, an agent useful as achemotherapeutic. Examples of active compounds include, but are notlimited to, ricin (or more particularly the ricin A chain),aclacinomycin, diphtheria toxin, Monensin, Verrucarin A, Abrin,Tricothecenes, Pseudomonas exotoxin A, taxol, cytochalasin B, gramicidinD, ethidium bromide, emetine, mitomycin, etoposide, tenoposide,anti-mitotic agents such as the vinca alkaloids (e.g., vincristine andvinblastine), colchicin, anthracyclines such as doxorubicin anddaunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin,actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine,tetracaine, lidocaine, propranolol, and puromycin and analogs orhomologs thereof, antimetabolites (e.g., methotrexate, 6-mercaptopurine,6-thioguanine, cytarabine, and 5-fluorouracil decarbazine), alkylatingagents (e.g., mechlorethamine, thioepa chlorambucil, melphalan,carmustine (BSNU), lomustine (CCNU), cyclothosphamide, busulfan,dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamineplatinum (II) (DDP)), and antibiotics, including but not limited to,dactinomycin (formerly actinomycin), bleomycin, mithramycin,calicheamicin, and anthramycin (AMC).

“Cytotoxic nucleoside or nucleotide” as used herein includes, but is notlimited to, 2′,2′-difluorodeoxycytidine, (dFdC, gemcitabine),5-fluorouracil (5-FU), 5-fluoro-2′-deoxyuridine-5′-O-monophosphate(FdUMP) or polymeric forms thereof (e.g., FdUMP[9] or FdUMP[10]),5-fluoro-2′-deoxyuridine (FdU), arabinosylcytosine (Ara-C), arabinosyladenosine (Ara-A), fluorouracil arabinoside, mercaptopurine riboside,5-aza-2′-deoxycytidine, arabinosyl 5-azacytosine, 6-azauridine,azaribine, 6-azacytidine, trifluoro-methyl-2′-deoxyuridine, thymidine,thioguanosine, 3-deazautidine, 2-Chloro-2′-deoxyadenosine (2-CdA), AZT(azidothymidine), 2′,3′-dideoxyinosine (ddI), cytotoxicnucleoside-corticosteroid phosphodiester, 5-bromodeoxyuridine5′-methylphosphonate, 5-fluorodeoxyuridine (FdUrd), fludarabine(2-F-ara-AMP), 6-mercaptopurine and 6-thioguanine,2-chlorodeoxyadenosine (CdA), 2′-deoxycoformycin (pentostatin),4′-thio-beta-D-arabinofuranosylcytosine, and any other cytotoxic dA, dC,dT, dG, dU, or homologs thereof; or combinations of any of the above.See U.S. Pat. No. 5,457,187 (Gmeiner et al.); U.S. Pat. No. 5,614,505(Gmeiner et al.); U.S. Pat. No. 5,663,321 (Gmeiner et al.); U.S. Pat.No. 5,741,900 (Gmeiner et al.); and U.S. Pat. No. 6,342,485 (Gmeiner).

“Cell of interest” as used herein may be any suitable cell, including,but not limited to, cancer cells, tissue cells (e.g., muscle, bone,nerve, liver, lung, etc.), pathological and non-pathological microbialcells (e.g., bacterial, mycobacterial, spirochetal rickettsial,chlamydial, mycoplasmal, and fungal, etc.), parasitic cells (e.g.,protozoal, helminth, etc.), and plant cells, etc.

“Cancer cell” as used herein may be any inappropriately proliferatingcell, including, but not limited to, cancerous cells of the lung, colon,ovarian, prostate, bone, nerve, liver, leukemia, and lymphoma, whichcells may be malignant or benign.

“Extracellular surface protein” as used herein may be any proteinwherein at least a portion of the protein is expressed on theextracellular surface of a cell of interest, including, but not limitedto, growth factor receptors, receptor tyrosine kinases, folatehydrolases, GPI-anchored cell surface antigens, pumps, and cell surfacereceptors including, but not limited to, G-protein coupled receptors,ion channel-linked receptors, and enzyme-linked receptors. In someembodiments, extracellular surface proteins of interest are those“differentially expressed” by upregulation of expression in a targetedcell of interest, in comparison to cells that are not specificallytargeted by a cytotoxic nucleotide.

For example, cancer cells differ from normal cells in many respects,including the up- or down-regulation of numerous genes. Among the genesthat are differentially expressed and/or regulated in cancer cells aregenes that encode proteins that are expressed on the extracellularsurface. As an example, specific proteins are expressed on theextracellular surface of prostate cancer (PC) cells that are notexpressed (or are expressed at very low levels) by normal prostaticepithelial cells and cells from other normal tissues. Extracellularproteins that are expressed exclusively by PC cells are excellentcandidates for specific targeting of malignant cells with anticancerdrugs. As an example, the expression of prostate specific membraneantigen (PSMA) is limited to PC cells and cells of the tumorneovasculature (Schulke et al., Proc. Natl. Acad. Sci. USA 100:12590-12595 (2003)). A second protein that displays characteristicssuitable for developing targeted therapeutics for PC is prostate stemcell antigen (PSCA; Saffran et al. 2001, Proc. Natl. Acad. Sci. USA 98:2658-2663). Other examples of proteins differentially expressed by somecancers are carbonic anhydrases (CA), such as CA IX and CA XI (See U.S.Pat. No. 5,589,579 to Bollon et al.), epidermal growth factor receptor(EGFR, also known as ErbB or HER) (Li et al. 2005, Cancer Cell7(4):301-311), etc.

“Prostate specific membrane antigen” or “PSMA” is a protein of interestin some embodiments for selective delivery of therapeutics for cancertreatment as a consequence of its elevated expression on the apicalplasma membrane of prostate cancer cells (Christiansen et al. 2005, Mol.Cancer Ther. 4: 704-714) and in endothelial cells of vasculature fromdiverse malignancies. PSMA is expressed by prostate epithelial cells(Gong et al. 1999, Cancer Metastasis Rev. 18: 483-490); however,elevated PSMA expression occurs in advanced prostate cancer (PCa),including bone metastases (Mannweiler et al. 2009, Pathol. Oncol. Res.15: 167-172) and PSMA expression levels are an independent predictor ofPCa recurrence (Perner et al. 2007 Hum. Pathol. 38: 696-701). PSMA isalso expressed in vasculature (Liu et al. 1997, Cancer Res. 57:3629-3634) from many different cancers including a high percentage ofbladder (Samplaski et al. 2011, Mod. Pathol. 24: 1521-1529), gastric andcolorectal (Haffner et al. 2009, Hum. Pathol. 40: 1754-1761), as well ashepatocellular, renal, breast, and ovarian cancer (Denmeade et al. 2012,Sci Transl Med 4: 140ra86-140ra86). PSMA is expressed as a dimer(Schülke et al. 2003, Proc. Natl. Acad. Sci. U.S.A. 100: 12590-12595),and dimerized ligands targeting the PSMA-dimer display improved activityrelative to monovalent ligands (Aggarwal et al. 2006, Cancer Res. 66:9171-9177).

In some embodiments, extracellular proteins that form dimers arepreferred targets. Examples include, but are not limited to, PSMA,transferrin receptor, the zinc enzyme carbonic anhydrase XII(Whittington et al. 2001, PNAS 98(17):9545-9550), ErbB receptors (Zhanget al. 2007, J Clin Invest. 117(8):2051-2058), etc.

In some embodiments, extracellular proteins that are associated with thedevelopment of tumor neovasculature are preferred targets. PSMA andvascular endothelial growth factor (VEGF) are non-limiting examplethereof.

In accordance with the present disclosure, aptamer targeting of proteinsof interest may be particularly beneficial for delivery ofchemotherapeutic that are associated with serious systemic toxicities.For example, doxorubicin (or “Dox”) is among the most widely-usedchemotherapy drugs; however, treatment can result in serious systemictoxicities, such as lethal cardiotoxicity, that may manifest years aftertreatment.

The A10-3 RNA aptamer, which can target PSMA, has been used to deliverdiverse therapeutic modalities selectively to cancer cells, includingcisplatin (Dhar et al. 2008, PNAS 105: 17356-17361; Dhar et al. 2011,PNASdoi:10.1073/pnas.1011379108.), functionalized nanoparticles (Gu etal. 2009, Methods Mol. Biol. 544: 589-598), a micelle-encapsulatedPI3K-inhibitor (Zhao et al. 2012, Mol. Pharm. 9: 1705-1716), as well astoxins (Chu et al. 2006, Cancer Res 66: 5989-5992) and siRNA (Ni et al.2011, J. Clin. Invest. 121: 2383-2390; Dassie et al. 2009, Nat.Biotechnol. 27: 839-849).

However, current RNA aptamers are costly to produce, require modifiednucleotides for nuclease stability, and toxins are generallynon-covalently associated with the aptamer. Non-covalent complexes oftoxins with duplex DNA typically have limited stability, with half-livesof only a few minutes (or less), and it is unlikely that non-covalentcomplexes of toxins with aptamers would be sufficiently stable foroptimal in vivo activity.

Pharmaceutical compositions taught herein may be used for the diagnosisand/or treatment of human subjects, or animal subjects for veterinary ordrug development purposes. Examples of animal subjects include mammalian(e.g., dog, cat, mouse, rat, horse, cow, pig, sheep, etc.), reptile,amphibian, and avian (e.g., parrot, budgie, chicken, turkey, duck,geese, quail, pheasant) subjects. “Treat” or “treatment” as used hereinrefers to an action resulting in a reduction in the severity of asubject's disease or condition, a delay in the progression of thedisease or condition, etc.

I. Aptamers and Methods for their Selection

“Aptamer” as used herein refers to a single-stranded nucleic acid (RNA,DNA, or modified forms thereof) whose distinct nucleotide sequencedetermines the folding of the molecule into a unique three-dimensionalstructure. Nucleic acid aptamers typically comprise a degenerate orrandom sequence flanked by fixed sequences onto which primers may bindfor amplification. Modified DNA and/or RNA bases may be used orincorporated as desired, e.g., beta-D-Glucosyl-Hydroxymethyluracil. See,e.g., U.S. Pat. No. 7,329,742. The nucleic acids may include anycombination of naturally-occurring nucleosides (A, G, C, T, U), and/ornucleoside or nucleotide analogs and/or derivatives as are well known inthe art, including cytotoxic, synthetic, rare, non-natural bases oraltered nucleotide bases. In addition, a modification can beincorporated to reduce exonucleolytic degradation, such as a reverse(3′→5′) linkage at the 3′-terminus.

In some embodiments, aptamers are selected for specific binding to atarget of interest such as an extracellular protein as described herein.For such selection, a pool of nucleic acids may be provided from whichcandidate aptamers are selected. A first pool of nucleic acids may becomprised of range of about 10⁶, 10⁸, 10¹⁰, 10¹¹, 10¹², or 10¹³, to arange of about 10¹⁴, 10¹⁵, 10¹⁶, 10¹⁸, 10²⁰, 10²¹, 10²², or 10²³ nucleicacid species. In some embodiments, the first pool of nucleic acidscomprises about 10¹⁰ to 10¹⁸ nucleic acid species. In some embodiments,the first pool of nucleic acids comprises about 10¹³ to 10¹⁴ nucleicacid species. In some embodiments, the first pool of nucleic acidscomprises 10¹⁵ nucleic acid species.

The size of the nucleic acid species within the first pool in someembodiments may be in a range of about 30 nucleotides to about 150nucleotides.

In preferred embodiments, the nucleic acid species of the presentinvention comprises three regions: a “variable” region flanked on eachend by a “primer” regions: Region A and Region B.

The “primer” regions may be used for the annealing of PCR primers duringPCR amplification. The two primer regions, A and B, need not beidentical to each other, but typically comprise known nucleotidesequences. The lengths of the primer regions can be in a range of about8 nucleotides to about 35 nucleotides. In some embodiments, the lengthsof the primer regions are in a range of about 12 nucleotides to about 22nucleotides. The length of Region A need not be the same as the lengthof Region B, and each region may be modified in length and/or sequencebased on folding predictions or results following the identification ofoptimal variable regions.

In some embodiments as taught herein, one or both of the primer regionshave “mismatches” with respect to the sequence of the primer intendedfor use in PCT amplification, i.e., places in the nucleotide sequencewhere the primer sequence is not complimentary to the primer region ofone or more nucleic acid species in the aptamer pool. For example, eachof the primers may independently have 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10mismatches. In some embodiments, use of such mismatches results in anultimate selected aptamer that is shorter in length than the startinglength due to non-specific binding within the aptamer duringamplification.

The “variable” region of the nucleic acids species within the first pooltypically includes random arrangements of nucleotide sequences. Thosevariable regions that selectively bind to a target of interest areselected during the selection of a first subpopulation of interest, andmay be used in a second pool of nucleic acid species.

In some embodiments, there is a predetermined bias contained within theprimer and/or variable regions. The predetermined bias may be used, forexample, to facilitate the inclusion of particular cytotoxic nucleotidesand/or active compound binding sites. For instance, in some embodimentsthe first pool of nucleic acids may be biased by including a greaterrepresentation of one or more particular nucleosides (A, C, G, T, and/orU). In some embodiments, the nucleic acid pool may include a lesserrepresentation of one or more particular nucleosides (A, C, G, T, and/orU). In some embodiments as taught herein, the pool may include a greaterrepresentation of CpG, which are useful as binding sites for covalentattachment. In some embodiments, the nucleic acid pool may include aspecific sequence element that may confer antisense or antigeneproperties to all of the members of the resulting subpopulation.

In some embodiments, the lengths of the nucleic acid species within thefirst pool includes the “primer” regions, wherein the size of thenucleic acid species can be in a range of about 45 nucleotides to about130 nucleotides in length. In other embodiments, the size of the nucleicacid species within the first pool can be in a range of about 60nucleotides to about 100 nucleotides in length. In further embodiments,the size of the nucleic acid species within the first pool can be in arange of about 65 nucleotides to about 80 nucleotides in length. Anadditional embodiment of the present invention comprises a first pool ofnucleic acid species, wherein the size of the nucleic acid species isabout 70 nucleotides in length.

In some embodiments, the length of the variable regions within the firstpool may be about 10, 15, 20, 25, 30, 35 or 40 nucleotides to about 50,55, 60, 65, 70, 75, 80, 90, 100, or 105 nucleotides in length, inclusiveof any particular length within this range.

The step of selecting a first subpopulation of nucleic acids from thefirst pool, wherein the first subpopulation comprises at least onenucleic acid that binds specifically to the protein of interest, may bedone using any method standard in the art, including, but not limitedto, such methods as affinity chromatography, capillary eletrophoresis,field flow fractionation chromatography and surface plasmon resonance.The methods of capillary electrophoresis and field flow fractionationchromatography may be further combined with mass spectrometry to obtainsequence information on the selected first subpopulation of nucleicacids. The step of selecting may be performed once, or the nucleic acidsfrom the first pool may be subjected to additional rounds of selectionto identify those nucleic acids with high affinity for the proteintarget of interest.

Other methods of identifying nucleic acids that can be used as the firstnucleic acid herein include, but are not limited to, those described inU.S. Pat. Nos. 7,329,742; 7,312,325; 6,867,289; 6,858,390; and6,369,208, or variations thereof that will be apparent to those skilledin the art given the present disclosure.

“Amplification” or “amplify” as used herein means the construction ofmultiple copies of a nucleic acid sequence, or multiple copiescomplementary to the nucleic acid sequence, using at least one of thenucleic acid sequences as a template. The step of amplifying nucleicacids may be any method standard in the art for amplifying nucleic acidsincluding, but not limited to, polymerase chain reaction (PCR),self-sustained sequence replication, strand-displacement amplification,“branched chain” DNA amplification, ligase chain reaction (LCR) andQ-Beta replicase amplification (QBR). In some embodiments, the selectednucleic acids are amplified using PCR.

In some embodiments, selecting a second subpopulation comprising atleast one nucleic acid species from the first subpopulation includesselection of at least one nucleic acid species that is internalized by acell of interest. Such selection may make use of detection methods suchas fluorescence microscopy and flow cytometry, including, but notlimited to, fluorescent-activated cell sorting.

To aid in detection, the at least one nucleic acid from the firstsubpopulation may be labeled with a detectable label using methodsstandard in the art, wherein the detectable label can include, but isnot limited to, fluorescent dyes, fluorophores, chromophores, affinitylabels, metal chelates, chemically reactive groups, enzymes,radionuclides, electrochemically detectable moieties, and energyabsorbing or energy emitting compounds.

Fluorescent dyes that can be used with the present invention are anycapable of binding to nucleic acids as defined herein and include, butare not limited to, the coumarin dyes, acetyl azide, fluoresceinisothiocyanate, 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine,8-(6-aminohexyl)aminoadenosine 3′,5′-cyclicmonophosphate,bis(triethylammonium) salt, rhodamine dyes, sulfonyl chloride, CyDye™fluors, and carboxynaphtofluorescein. The haptenes that may be used forlabeling include, but are not limited to, biotin, digoxigenin, and2,4-dinitrophenyl. The haptenes require fluorescently-labeled antibodiesor specific proteins for visualization/detection.

Sequencing at least one selected nucleic acid from a secondsubpopulation may be done according to methods standard in the artincluding, but not limited to, automated nucleic acid sequencingprocedures as disclosed in Naeve, C. W., (1995) Biotechniques 19:448,and sequencing by mass spectrometry. See, e.g., PCT InternationalPublication No. WO 94/16101; Cohen et al., Adv. Chromatogr. 36:127-162(1996); and Griffin et al., Appl. Biochem. Biotechnol. 38:147-159(1993).

Synthesizing a nucleic acid having a sequence corresponding to aselected aptamer may be done according to any method standard in the artincluding, but not limited to, de novo chemical synthesis ofpolynucleotides, such as by presently available automated DNAsynthesizers, and standard phosphoramidite chemistry. De novo chemicalsynthesis of a polynucleotide can be conducted using any suitablemethod, including, but not limited to, the phosphotriester orphosphodiester methods. See Narang et al., Meth. Enzymol., 68:90 (1979);U.S. Pat. No. 4,356,270; Itakura et al., Ann. Rev. Biochem., 53:323-56(1989); Brown et al., Meth. Enzymol., 68:109 (1979); and U.S. Pat. No.6,911,310 issued to Heller. For example, automated nucleic acidsynthesis may be conducted using an Applied Biosystem 394™ automatedDNA/RNA synthesizer (Applied Biosystems, Foster City, Calif.).

II. Incorporation of Active Compounds

In some embodiments, one or more active compounds are incorporated intoand/or covalently bound to the aptamer, after and/or during selection.

In some embodiments, the covalent binding comprises a geminal diaminelinkage. A “geminal diamine linkage” refers to a group comprising themoiety —NHCRR′NH—, wherein R and R′ are each independently hydrogen oralkyl (e.g., C1-C6 alkyl), the moiety having two points of attachment asshown. An illustrative example of a compound having a geminal diaminelinkage is the compound N-butyl-N-ethylmethanediamine

For example, an anthracycline such as doxorubicin may be covalentlybound to a CpG site in a nucleic acid such as an aptamer as taughtherein with the formation of a Schiff base 1 (e.g., by reaction withformaldehyde). Intercalation of the doxorubicin Schiff base andsubsequent reaction of the Schiff base with the 2-amino group of aguanine allows for the formation of a geminal diamine 2, as depictedbelow in Scheme 1.

Compound 2 may be further stabilized in the double-stranded nucleic acidby hydrogen bonding of the doxorubicin tertiary alcohol to a second2-amino group of a deoxyguanosine on the other strand. This complex isdepicted below as structure 3. See also Fenick et al. 1997, Doxoform andDaunoform: Anthracycline-Formaldehyde Conjugates Toxic to ResistantTumor Cell. J. Med. Chem., 40:2452-2461.

Transport of complex 3 to the endosome exposes complex 3 to an acidicenvironment, which facilitates the protonation of the geminal diamine(pKa of the doxorubicin amino group is 8.2). Spontaneous decompositionof the protonated geminal diamine in the endosome leads to the formationof active doxorubicin within the cell, as shown in Scheme 2.

The geminal diamine linkage useful for covalent active compoundattachment is readily released under moderately acidic conditions (e.g.,pH<6.8, 6.5, 6.2, 6, 5.8, etc.) that typically occur in endosomesfollowing cellular internalization, or possibly in the tumormicroenvironment. The active compound so released can diffuse away fromthe aptamer and effect its therapeutic target, e.g., reacting with hostcell DNA.

Further, the reductive activation of an anthracycline such asdoxorubicin or daunorubicin can lead to the production of dioxygenspecies such as superoxide and hydrogen peroxide, which may, in turn,oxidize constituents in the medium to formaldehyde via Fenton chemistry.See, Fenick et al. 1997, J. Med. Chem., 40:2452-2461. Formaldehydeproduced in the cell may then react with the anthracycline, and theformed Schiff base can react with host cell DNA.

For example, an active compound such as doxorubicin so released readilytranslocates to the nucleus and is capable of exerting cytotoxicity to asimilar extent as free doxorubicin, which acts via Topoisomerase 2poisoning. Formaldehyde released from the upon acid-mediateddissociation may promote binding to genomic DNA (Swift et al. 2002, Mol.Cancer Ther. 2: 189-198; Wang et al. 1991, Biochemistry 30: 3812-3815).Thus, formaldehyde is not merely a passive chemical linkage, but mayalso potentiate genomic DNA binding of an active compound released fromthe aptamer.

In some embodiments, the active compound may be a taxane, particularly ataxane having a free amine, such as paclitaxel and docetaxel. See Sajjadet al., Applied radiation and Isotopes 70:1624-1631 (2012). Such taxanesmay be covalently conjugated to the aptamer in a similar manner as thatdescribed above for doxorubicin.

In some embodiments, it is preferred that the selected nucleic acidsequence substantially retains its original three-dimensional structureof the native sequence following the incorporation of the activecompounds. Folding calculations may be performed to compare thepredicted folding patterns of the chemical structure of the nativenucleic acid sequence with that of a nucleic acid sequence incorporatingone or more active compounds. Calculations can be performed with, e.g.,folding programs such as mFOLD (Michael Zuker, Burnet Institute). Suchcalculations apply an algorithm to the native sequence of the nucleicacid to determine folding patterns that yield the most stable secondarystructures. This approach provides insight into the likely location ofdouble helical regions that occur within the three-dimensional structureof the nucleic acid. The structural characteristics of the native andmodified nucleic acids can also be determined using circular dichroism(CD) spectroscopy and ultraviolet (UV) hyperchromicity measurements.Other methods of comparison will be apparent to those skilled in theart. In some embodiments, preferred nucleic acids of interest are thosethat incorporate compounds of interest in such a way as to notsignificantly or unduly alter the folding characteristics and/orultimate three-dimensional structure of the native sequences.

In some embodiments, aptamers incorporating one or more active compoundsmay be further evaluated for the extent to which they selectively killcells of interest, e.g., through the release of cytotoxic nucleotides by3′-O-exonucleolytic degradation. Cell viability can be evaluated, e.g.,using 3-(4,5-dimethythiazole-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium,inner salt (MTS) assays. Preferred nucleic acids are those that arecytotoxic towards cells of interest and not cytotoxic to non-targetedcells.

III. Dimeric Aptamers

In general, “dimeric” aptamers as described herein are compounds of thegeneral formula A-B-C, wherein:

A is a first aptamer that specifically binds to or targets anextracellular surface protein of interest,

B is a linker (e.g., nucleic acid linker and/or alkyl linker, etc.); and

C is a second apatmer that specifically binds to or targets anextracellular surface protein of interest, which aptamer can be the sameas, or different from, the first aptamer A, and/or specifically binds ortargets the same or a different protein of interest.

An “alkyl linker” or “alkyl spacer,” used interchangeably herein, may,for example, be a partially saturated or fully saturated C2, C3, C4, orC5, to C6, C7, C8, C9 or C10 alkyl group, which group may be linear orbranched. The linker may be of any suitable length, for example, 10, 20or 50 Angstroms in length, up to 100, 200 or 500 Angstroms in length, ormore, considering the targets of aptamer A and aptamer B and how theyare expressed and/or dimerized by a cell of interest.

A “nucleic acid linker” or “nucleic acid spacer,” used interchangeablyherein, may be any suitable nucleic acid, and in some embodiments isdouble stranded in whole or in part in the formed dimeric aptamer (see,e.g., FIG. 1). In some embodiments, the nucleic acid linker is providedby hybridizing complimentary ends of each of the two apatmers in thedimeric pair. In some embodiments, the nucleic acid linker may be apoly-T/poly-A linker (optionally with some or all of the poly-T replacedby poly-FdU). In some embodiments, the nucleic acid linker may includeone or more CpG binding sites useful for covalent binding of an activecompound as taught herein.

One or more alkyl linker(s) may also be included within the nucleic acidlinker, which in some embodiments provides flexibility (e.g., rotationalflexibility) of the complex, which may result in a higher bindingaffinity. See also, U.S. Patent Application Publication No. 2010/0261781to Gmeiner.

In some embodiments, a double-stranded nucleic acid spacer has asequence that is sufficiently thermally stable such that the dimericaptamer remains dimeric under physiological conditions (e.g., having amelting temperature of at least 35, 37, 40, 45, 50, 55, 60, or 65degrees Celsius in a solution isotonic with blood or other tissues),preferably for times sufficient for the dimeric aptamers to localizespecifically to targets in vivo, considering the formulation and/orroute of administration.

IV. Formulations and Routes of Administration

The aptamers as taught herein may be formulated for administration in apharmaceutical carrier in accordance with known techniques. See, e.g.,Remington, The Science And Practice of Pharmacy (9^(th) Ed. 1995). Inthe manufacture of a pharmaceutical formulation according to theinvention, the aptamer may be admixed with, inter alia, an acceptablecarrier. The carrier must, of course, be acceptable in the sense ofbeing compatible with any other ingredients in the formulation and mustnot be unduly deleterious to the patient. The carrier may be a solid ora liquid, or both, and is preferably formulated as a unit-doseformulation with respect to the aptamer and/or active compound payload,for example, a tablet, which may contain from 0.01 or 0.5% to 95% or 99%by weight of the active compound(s).

Formulations of the invention include those suitable for oral, rectal,topical, buccal (e.g., sub-lingual), vaginal, parenteral (e.g.,subcutaneous, intramuscular, intradermal, or intravenous), topical(i.e., both skin and mucosal surfaces, including airway surfaces) andtransdermal administration, inclusive of intra-tumoral administration,although the most suitable route in any given case will depend on thenature and severity of the condition being treated and on the nature ofthe particular active compound being used.

Formulations suitable for oral administration may be presented indiscrete units, such as capsules, cachets, lozenges, or tablets, eachcontaining a predetermined amount of the aptamer and/or activecompound(s); as a powder or granules; as a solution or a suspension inan aqueous or non-aqueous liquid; or as an oil-in-water or water-in-oilemulsion. Such formulations may be prepared by any suitable method ofpharmacy which includes the step of bringing into association the activecompound and a suitable carrier (which may contain one or more accessoryingredients as noted above). In general, the formulations of theinvention are prepared by uniformly and intimately admixing the activecompound with a liquid or finely divided solid carrier, or both, andthen, if necessary, shaping the resulting mixture. For example, a tabletmay be prepared by compressing or molding a powder or granulescontaining the active compound, optionally with one or more accessoryingredients. Compressed tablets may be prepared by compressing, in asuitable machine, the compound in a free-flowing form, such as a powderor granules optionally mixed with a binder, lubricant, inert diluent,and/or surface active/dispersing agent(s). Molded tablets may be made bymolding, in a suitable machine, the powdered compound moistened with aninert liquid binder.

Formulations suitable for buccal (sub-lingual) administration includelozenges comprising the active compound in a flavoured base, usuallysucrose and acacia or tragacanth; and pastilles comprising the compoundin an inert base such as gelatin and glycerin or sucrose and acacia.

Formulations of the present invention suitable for parenteraladministration comprise sterile aqueous and non-aqueous injectionsolutions, which preparations are preferably isotonic with the blood ofthe intended recipient. These preparations may contain anti-oxidants,buffers, bacteriostats and solutes which render the formulation isotonicwith the blood of the intended recipient. Aqueous and non-aqueoussterile suspensions may include suspending agents and thickening agents.The formulations may be presented in unit\dose or multi-dose containers,for example sealed ampoules and vials, and may be stored in afreeze-dried (lyophilized) condition requiring only the addition of thesterile liquid carrier, for example, saline or water-for-injectionimmediately prior to use. Extemporaneous injection solutions andsuspensions may be prepared from sterile powders, granules and tabletsof the kind previously described. For example, in one aspect of thepresent invention, there is provided an injectable, stable, sterilecomposition comprising an aptamer and/or active compound(s) in a unitdosage form in a sealed container. The aptamer and/or active compound(s)may be provided in the form of a lyophilizate which is capable of beingreconstituted with a suitable pharmaceutically acceptable carrier toform a liquid composition suitable for injection thereof into a subject.The unit dosage form typically comprises from about 10 mg to about 10grams of the active compound(s). When the active compound(s) issubstantially water-insoluble, a sufficient amount of emulsifying agentwhich is physiologically acceptable may be employed in sufficientquantity to emulsify the compound or salt in an aqueous carrier. Onesuch useful emulsifying agent is phosphatidyl choline.

Formulations suitable for rectal administration are preferably presentedas unit dose suppositories. These may be prepared by admixing the activecompound with one or more conventional solid carriers, for example,cocoa butter, and then shaping the resulting mixture.

Formulations suitable for topical application to the skin preferablytake the form of an ointment, cream, lotion, paste, gel, spray, aerosol,or oil. Carriers which may be used include petroleum jelly, lanoline,polyethylene glycols, alcohols, transdermal enhancers, and combinationsof two or more thereof.

Formulations suitable for transdermal administration may be presented asdiscrete patches adapted to remain in intimate contact with theepidermis of the recipient for a prolonged period of time. Formulationssuitable for transdermal administration may also be delivered byiontophoresis (see, for example, Pharmaceutical Research 3 (6):318(1986)) and typically take the form of an optionally buffered aqueoussolution of the active compound. Suitable formulations comprise citrateor bis\tris buffer (pH 6) or ethanol/water and contain from 0.1 to 0.2Mactive ingredient.

The present invention is further exemplified by the followingnon-limiting examples.

EXAMPLES

A new strategy was developed for improved targeted delivery ofdoxorubicin (Dox) to PSMA+ cancer cells using a novel dimeric DNAaptamer complex bound to Dox through a pH-sensitive linker. PSMA isexpressed on the plasma membrane as a dimer, and dimerized ligandstargeting PSMA display improved activity relative to monovalent ligands(Aggarwal et al. 2006, Cancer Res. 66: 9171-9177). Dimeric aptamercomplex (DAC) take advantage of the dimeric nature of PSMA.

5′-dCpG, the preferred binding site for Dox, was interspersed in theprimers used for PCR amplification during SELEX to permit Dox-bindingmotifs to be retained in the final DNA aptamer sequence (FIG. 1).Priming sequences were imperfectly matched to fixed sequences within thetemplate, permitting aptamer length to vary during the selectionprocess.

Identified was a 48-nucleotide DNA aptamer (SZTI01) using an affinitymatrix consisting of the extracellular domain of human PSMA.

Results

Thermal Stability of Dimeric Aptamer Complexes. A duplex DNA “bridge”was used to link the two DNA aptamers in the DAC (FIG. 1). The bridgingDNA duplex was designed to be sufficiently thermally stable such thatthe dimeric aptamer complex (DAC) remains intact under physiologicalconditions for times sufficient for aptamers to localize specifically totargets in vivo, and includes a preferred site for Dox binding (CpG).The fixed sequences used during the aptamer selection process alsoincluded preferred sites for Dox binding that are included in the finalDAC structure.

Thermal melting profiles were obtained for DACs with and without Doxmodification to evaluate stability of these complexes and any effectsDox may have on thermal stability (FIG. 2). The temperature-dependent UVmelting profile for the dA16:T16 DAC indicated some reduction insecondary structure at temperatures less than 30° C. with initialdissociation of the dimeric complex at ˜41° C. with a dissociationtemperature of ˜47° C. While dissociation for this dimeric complexoccurred above physiological temperature, increased stability wasdesired to promote long-term stability under physiological conditions.Further, the A-T duplex used to form this dimeric complex did notinclude a Dox-binding sequence motif.

To address these issues, an alternative dimeric aptamer complex (DAC)was prepared by appending GCCG and CGGC sequences to the 5′- and 3′-endsof the A16:T16 DNA duplex forming sequences (FIG. 1). The resulting DACdisplayed a dissociation temperature of ˜58° C., thus displayingstability suitable for further development. Covalent modification of DACwith Dox (DAC-D) further enhanced complex stability, and the DAC-Dcomplex displayed minimal change in absorbance for temperatures lowerthan the Tm consistent with Dox stabilizing DAC structure (FIG. 2a ).

The secondary structure and thermal stability of DAC were furtherinvestigated using CD spectroscopy. The DAC complexes displayed CDspectra typical of B-form DNA with a maximum at 283 and a minimum at 248nm consistent with the tail-forming sequences forming the targetstructures. Covalent modification with Dox in the DAC-D complex has nodiscernible effect on overall secondary structure for the complexalthough a slight sharpening in the peaks was noted. The DAC-D complexdisplayed less sensitivity to increased temperature relative to DAC andDAC+Dox, indicating that covalent modification with Dox stabilizes theoverall complex.

Formation and Dissociation of Covalent Dox-Conjugates. The duplex DNAbinding motif stabilizing the DAC has the potential for binding twoequivalents of Dox per complex. In addition, the DNA aptamers comprisingthe complex contained other CpG sites for potential Dox binding (FIG.1). A covalent complex was formed between the DAC and Dox (DAC-D) bymixing the dimeric complex with a four-fold excess of Dox in thepresence of formaldehyde. Covalent linkages were formed at 4:1stoichiometry (Table 1), and Dox transfer from the resulting covalentcomplex (DAC-D) was evaluated in which Dox fluorescence is effectivelyquenched, to an excess of a 25 mer DNA hairpin in which Dox fluorescenceis less effectively quenched. These studies revealed the half-life forDox covalently bound in DAC-D via formaldehyde was >8 h (FIG. 2b ). Incontrast, the dissociation of the non-covalent complex was too rapid tomeasure using this assay, but is fully dissociated in ≤5 minutes. Thesestudies indicated that covalent attachment of Dox results in formationof a complex with greatly increased retention of Dox that is well-suitedfor drug delivery applications in vivo.

TABLE 1 Absorbance values for DAC-D complexes of different aptamer:Doxratio. Dox DNA Abs at Abs at Conc Conc 498 nm 260 nm (μM) (μM) Dox:DNADAC-D 1 0.0358 1.0223 3.48 0.793 4.388398 DAC-D 2 0.0272 1.0084 2.850.768 3.710938 DAC-D 3 0.0376 1.61 4.02 1.19 3.378151 avg 3.825829 stddev 0.51483

PSMA-Specific Uptake of Dimeric Complexes. The selective delivery of Doxto PSMA+ cells requires binding and ideally internalization of thecomplex. To evaluate to what extent the DAC was specific for binding andinternalization into PSMA+ cells, internalization of the complex inPSMA+ C4-2 cells and PSMA-null PC3 cells was compared using confocalmicroscopy and flow cytometry. The component of the dimeric complexcontaining dA16 ssDNA was labeled with Quasar 570 while the componentwith T16 ssDNA was labeled with Quasar 670, permitting simultaneousdetection and visualization of each aptamer component. Confocalmicroscopy revealed minimal uptake of either fluorescently-labeledaptamer into PC3 cells; however strong signal was observed for eachfluorescent aptamer signal in PSMA+ C4-2 cells. Further, fluorescenceemitted from each of the two aptamers was completely co-localizedconsistent with uptake and retention of the DAC in dimeric form.Fluorescence emitted from the aptamer complexes appeared punctate, withnuclear exclusion, consistent with endosomal localization of the DAC,which was confirmed by co-localization with the endosomal markerFITC-dextran. Flow cytometry also confirmed specificity of DAC for PSMA+C4-2 cells (FIG. 3). Pre-incubation of C4-2 cells with J591PSMA-specific monoclonal antibody attenuated DAC uptake consistent withPSMA-specific internalization.

PSMA-Specific Delivery of Dox. The serious toxicities associated withDox treatment indicate that premature release of Dox from targetingvehicles is likely to be therapeutically detrimental. In this regard,non-covalent complexes of Dox with DNA have demonstrated improvedtoxicity profiles relative to free Dox (Trouet and Jones 1984, Semin.Oncol. 11: 64-72); however covalent linkage of Dox with a targetedDNA-vehicle should markedly enhance efficacy and reduce systemictoxicities by limiting Dox-dissociation while in circulation.

A strategy was developed to covalently attach Dox to the DAC usingformaldehyde, a method previously shown to promote covalent complexformation of Dox with genomic DNA (Zeman et al. 1998, Proc Natl Acad SciUSA 95: 11561-11565). The specific delivery of Dox to PSMA+ cells usingDAC-D was evaluated using confocal microscopy. While non-complexed Doxreadily accumulated in the nuclei of both PC3 and C4-2 cells, Doxdelivered using DAC-D internalized nearly exclusively into C4-2 cellswith minimal accumulation in PC3 cells. Dox fluorescence was exclusivelynuclear, while the aptamer fluorescent signal from DAC-D displayednuclear exclusion consistent with Dox becoming dissociated from theDAC-D following cellular internalization.

These results are consistent with Dox becoming dissociated in the acidicenvironment of the endosome following cell-uptake of DAC-D followed bynuclear localization of Dox. The results thus confirm PSMA-specificuptake of the DAC-D complex with nuclear delivery of Dox.

PSMA-Dependent Selective Cytotoxicity. The specificity of DAC-D forPSMA+ cells was evaluated using cell-viability assays in PC3 and C4-2cells. The results are shown in FIG. 4. Free-Dox was highly cytotoxic toboth PC3 and C4-2 cells consistent with the wide-spectrum activitypreviously reported. In contrast, Dox delivery via DAC-D was highlycytotoxic towards C4-2 cells, but displayed greatly reduced cytotoxicityto PC3 cells. For example, at Dox concentrations that resulted in ˜90%reduction in viability for free-Dox (2 μM), the same amount of Doxdelivered via DAC-D displayed greater than 80% potency towards targetedC4-2 cells and less than 50% of cytotoxic activity towards PC3 cells.

An especially challenging situation for targeted drug delivery occurswhen targeted cells are in close proximity to non-malignant cells asarises in metastases to vital organs. In this case, highly localizedcytotoxicity is desirable. To simulate this challenging environment, weperformed co-culture of luciferase-transfected C4-2 cells (C4-2-luc)with PC3 cells and assessed the viability of each cell line inco-culture independently (FIG. 4). Preliminary studies demonstrated thatC4-2-luc and C4-2 cells displayed no significant difference in viabilityin response to Dox or the DAC-D complex. The response of C4-2-luc cellsin co-culture with PC3 cells was similar to C4-2 cells in mono-culturewith DAC-D retaining greater than 80% cytotoxicity in the mixedenvironment. In contrast, PC3 cells in co-culture with C4-2-luc cellsshowed markedly decreased response to DAC-D relative to studies inmonoculture (p<0.05). The results are consistent with the DAC-Dundergoing selective internalization into targeted PSMA+ C4-2 cells,reducing the DAC-D available for non-specific uptake into non-targetedPC3 cells.

Discussion

Aptamer-mediated delivery is a promising technology for improving thetherapeutic index of cytotoxic drugs that cause serious systemictoxicities, such as Dox. A new DNA aptamer to PSMA was identified anddeveloped a dimeric aptamer complex (DAC) to take advantage of PSMAbeing expressed as a dimer. The objective was to use the DAC as ascaffold for high-capacity drug delivery. The process used for aptameridentification was designed to identify DNA sequences that includedpreferred Dox binding sites (e.g., 5′-CpG). Also developed was a processfor covalent modification at the preferred binding sites with Doxresulting in a high capacity (4:1) payload. The covalent linkageutilized is pH-sensitive releasing free Dox in the acidic environment ofendosomes following internalization into targeted cells. Released Doxmigrates to the nucleus and binds genomic DNA interfering in replicationand mitosis while the DAC is retained in the cytosol. The resultantDAC-D complex is internalized selectively into PSMA+ cells and is highlycytotoxic to these cells while displaying minimal effects to PSMA-nullcells. This high degree of selectivity is retained in the context ofco-culture experiments in which PSMA+ cells retain full sensitivity tothe targeted complex even while co-cultured adjacent PSMA-null cells arenot affected. Based on these data, it is expected that DAC-D complexeswill be highly effective anti-tumor agents in vivo with minimal systemictoxicity.

Dimeric aptamer complexes have potential advantages relative tomonomeric aptamers for drug delivery applications in terms of targetselection, target avidity, physical and chemical stability, higherpayload capacity, improved pharmacokinetics, and utility if partlydamaged, among other properties. The present studies utilized a DAC withboth components targeting PSMA which is expressed as a dimer.

The length of the 24 base pair DNA duplex connecting the componentaptamers is approximately 70 Å, which is similar to the dimensions ofthe PSMA dimer, making it possible for the component aptamers to bindsimultaneously, although optimization of DAC dimensions would berequired to fully optimize simultaneous binding. The structure of theDAC utilized in the present studies was stable under physiologicallyrelevant conditions and useful for high-capacity drug delivery with a4:1 stoichiometry payload. In principle, additional Dox binding sitescan be included into the structure to further enhance drug-deliverypotential.

The chemical linkage used for covalent Dox attachment enables convenientsynthesis with high yields and straightforward purification. While thisapproach is readily scaled for in vivo studies and eventual clinicalapplications, one of the more important advantages of using thischemistry for Dox delivery, in particular, is that Dox is readilyreleased from the DAC-D under moderately acidic conditions (pH<6) thatoccur in endosomes following cellular internalization, or possibly inthe tumor microenvironment. Dox released from endocytic DACs readilytranslocates to the nucleus and is capable of exerting cytotoxicity to asimilar extent as free Dox which acts via Topoisomerase 2 poisoning.Formaldehyde released from the DAC-D upon acid-mediated dissociation hasthe potential to promote Dox binding to genomic DNA (Swift et al. 2002,Mol. Cancer Ther. 2: 189-198; Wang et al. 1991, Biochemistry 30:3812-3815.). Thus, formaldehyde is not merely a passive chemicallinkage, but may also potentiate genomic DNA binding of Dox releasedfrom the DAC-D delivery vehicle. This approach has advantages relativeto strategies that use covalent linkers that lack this potential forenhancing genomic DNA binding by released Dox.

The DAC-D described here has molecular weight (˜45 kDa) suitable forprolonged retention in plasma as well as tumor localization via the EPRand with specificity for malignant cells via PSMA targeting. Ultimately,DAC-D should prove useful for clinical management of cancer.

Material and Methods

DNA SELEX. Recombinant human PSMA extracellular domain (720 amino acids)was expressed from baculovirus (Kinakeet Biotechnology; Richmond, Va.).The recombinant protein included a His-tag sequence that was used toform an affinity matrix using Talon beads which was then used in a DNASELEX procedure to identify DNA aptamers to PSMA. DNA aptamers wereselected from a library including a 47 nucleotide random sequenceflanked by fixed sequences of 21 nucleotides each. The fixed sequencesselected permit formation of short hairpins in the final aptamer thatinclude stem regions with sequence elements favorable for Dox binding(underlined). The sequence for the random library was:

(SEQ ID NO: 1) dGCGAAAACGCAAAAGCGAAAA(N47)ACAGCAATCGTATGCTTAGCA

Initially 8 μg ssDNA from the random library (307 picomoles of DNA; 186trillion sequences) was converted to dsDNA using a T7 fill-in reactionand amplified by PCR using primers that were imperfectly matched to thetemplate.

(forward) (SEQ ID NO: 2) 5′ dGCGTTTTCGCTTTTGCGTTTT (reverse)(SEQ ID NO: 3) 5′ dAGCATTGCTATCGTAAGCAGA

The 5′-primer was synthesized with a 5′-phosphate and the resultingdsDNA was converted to ssDNA using λ-exonuclease to selectively cleavethe strand amplified with the phosphorylated primer. SELEX forwardrounds were performed by adding 1 mg of PSMA bound to Dynabeads Talon to700 μL of binding buffer (100 mM NaCl, 20 mM Tris, 2 mM MgCl2, 5 mM KCl,1 mM CaCl2, 0.2% Tween-20, pH 8). The beads were removed using a Dynalmagnet and were washed four times with binding buffer. At least 10 μg ofssDNA was annealed by heating to 95° C. followed by gentle cooling andwas added to the PSMA-matrix followed by vortexing and incubation for 1h at 37° C. with mild agitation. The supernatant was removed and 20 μLof 5 μM 5′-phosphorylated primer was added to the beads and the mixturewas heated to 95° C. for 5 min following which the beads weresequestered and the supernatant transferred to a clean microfuge tubeand DNA converted to dsDNA using a primer-extension reaction using T7polymerase. DNA was collected by ethanol precipitation and thenamplified by 10 cycles of PCR using a phosphorylated 3′-primer. ThedsDNA was purified by gel electrophoresis followed by ethanolprecipitation and then converted to ssDNA by treating 32-40 μg of dsDNAwith λ-exonuclease for 30 min at 37° C. followed by ethanolprecipitation. The resulting ssDNA was analyzed by gel electrophoresisand quantified by UV absorbance and used in a subsequent SELEX forwardor counter round. Counter rounds differed from forward rounds byincubation with a magnetic bead matrix that did not contain PSMA andusing the DNA that did not bind to the matrix for subsequent PCRamplification. A total of 10 forward and two counter rounds wereperformed. After the final SELEX round, ssDNA was converted to dsDNAusing a T7 fill-in procedure and was cloned into a pGEM vector (Promega)for sequencing. A single, 48 nucleotide sequence (SZTI01) was identifiedand used in subsequent studies.

SZTI₀₁: (SEQ ID NO: 4) dGCGTTTTCGCTTTTGCGTTTTGGGTCATCTGCTTACGATAGCAATGCT

PSMA-Specific Aptamer Synthesis: The DNA aptamer sequences weresynthesized at either the University of Calgary (Calgary, Canada) or IDTInc. (Coralville, Iowa). Aptamers were reconstituted in sterile,nuclease-free H₂O at 100 μM. Dimeric aptamer complexes were preparedfrom aptamers that included either a dA16 or T16 single-stranded tail atthe 3′-terminus (dA16:T16DAC) by mixing the 2 monomers at 1:1 ratiofollowed by heating to 95° C. and gentle cooling. The DAC used for thesestudies (unless otherwise indicated) included the sequences dCGGCA16GCCG(SEQ ID NO:5) or dCGGCT16GCCG (SEQ ID NO:6). The secondary structure forthe DAC calculated using m-fold is shown in FIG. 1.

Synthesis of DAC-D Complexes: The covalent complex of DAC with Dox(DAC-D) was prepared by mixing 250 μL of a 50 μM solution of the DACwith a Dox-formaldehyde solution prepared upon incubation of a 0.37%formaldehyde solution in Dulbecco's Phosphate Buffered Saline withoutCalcium or Magnesium (DPBS) pH 7.4 with Dox. The reaction proceeded in alight-free manner at 4° C. for 48 hours. The solution was extracted oncewith 300 μL of phenol:chloroform followed by two additional extractionswith 300 μL chloroform. The aqueous phase was then ethanol-precipitatedand the pellet rinsed 2× with 70% ethanol and once with absolute ethanoland dried under reduced pressure. The red pellet was re-suspended in 100μL dH₂O. Yields were typically >90% based on DNA recovery.

Determination of Dox:DNA Ratios: DNA samples were prepared in dH₂O, andabsorbencies were measured from 200-800 nm using a Beckman Coulter DU800spectrophotometer. A standard curve of Dox was established between 1 μMand 10 μM by using absorbencies at 494 nm at 85° C. To assess the amountof Dox covalently bound to DNA, the samples were heated to 85° C. beforemeasuring the absorbance at 494 nm and 260 nm. The 260 nm wavelength wasused to determine the DNA content in the sample and to determine theDox:DNA ratio.

Dox Transfer from DAC-D: Samples of DAC-D, or the non-covalent complex(DAC+D) or free Dox 625 nM were prepared in DPBS with or without a100-fold (by weight) excess of a 25 mer DNA and were incubated at 37° C.Changes in fluorescence intensity were determined using a Typhoon-9210variable mode imager with excitation set to 532 nm and the emissionfilter at 580 nm.

Temperature-Dependent UV Studies: Temperature-dependent UV absorptionspectra were obtained using a Beckman Coulter DU-800 UV-Visspectrophotometer. Samples of DAC, DAC-D, and DAC+D were prepared. Thetemperature was increased at a rate of 0.7° C./min over the range 20-85°C. and absorbance at 260 nm was measured for each sample, (400 μL, 1 μM)concentration.

Cell lines: The C4-2 cell line was a gift from Dr. Elizabeth M. Wilson(UNC, Chapel Hill, N.C.). C4-2Luc cell line was generated bytransfecting C4-2 cells with pTRE2hygro and firefly luciferase (PGL3).PC3 cells were purchased from cell and viral vector core laboratory atWake Forest School of Medicine. All cells were maintained with RPMI 1640(Gibco, Grand island, N.Y.) with 10% fetal bovine serum (GeminiBio-Products, West Sacramento, Calif.). All cells were kept at 5% CO₂ at37° C.

Confocal microscopy: Cells were seeded at 20,000 cells/well in 8-wellLab-Tek® II chambered #1.5 German coverglass system (Thermo Fisher Sci.,Waltham, Mass.), and incubated at 37° C. under 5% CO₂ for 2 days. Cellswere incubated with 1 μM of DAC in which the dA16 aptamer was labeledwith Quasar 570 at the 5′-terminus and the T16 aptamer was labeled withQuasar 670 dyes in RPMI with 10% FBS for 2 h at 37° C. Cells were washedwith fresh media and DPBS, followed by a 5 min fixation with 3.7%formaldehyde in DPBS. Cells were visualized using a Zeiss LSM510confocal microscope (Carl Zeiss, Oberkochen, Germany). Cells were alsoincubated with 1 μM of DAC-D (or the non-covalent DAC+D), for 2 h. DACwere only labeled with Quasar 670 for these studies as the Quasar 570emission would interfere with the Dox emission. Cells were washed,fixed, and imaged using identical procedures.

Flow cytometry: PC3 and C4-2 cells were incubated with 1 μM of DAC for 2h at 37° C. Dimers were fluorescently labeled with either Quasar 570 or670 alone, or both. Cells were trypsinized and washed with PBS twice.Cells re-suspended in PBS were analyzed to measure their intracellularfluorescence using the Accuri™ C6 flow cytometer (BD Biosciences).

Cytotoxicity measurements: PC3, C4-2, and C4-2Luc cells were seeded at adensity of 3,000 cells/well in 96-well plates and incubated at 37° C.under 5% CO₂. Next day, the cells were treated with Dox, DAC+Dox, orDAC-D for 24 h. Next day the treatment was removed, cells were washedonce with warm fresh media and incubated for another 48 h in freshmedia. Cell counts were measured indirectly by measuring the ATP amountsusing CellTiter-Glo® luminescent cell viability assay (Promega, Madison,Wis.) according to the manufacturer's protocol. In co-cultureexperiments, PC3 and C4-2Luc cells were each seeded at a density of1,500 cells/well in 96-well plates. Co-cultured cells were treated withDox, DAC+Dox, or DAC-D and cell viability was also measured using theCellTiter-Glo® assay. Luciferase levels were measured for co-cultures ofPC3 and C4-2Luc cells using a luciferase reporter assay system(Promega). PC3 and C4-2Luc cells were seeded and treated as describedabove and the cells were lysed and luciferase activity was measuredaccording to the manufacturer's protocol.

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Titration of Dimeric Aptamer Complex

Titration data (Table 2) confirms that 14 molar equivalents ofdoxorubicin can be covalently bound to each dimeric aptamer complex(DAC).

TABLE 2 Dox:DAC ratio DNA conc μm Dox Conc μm calc ratio 16× 0.201 2.1710.79602 24× 0.17 2.41 14.17647 32× 0.218 2.99 13.7156

The foregoing is illustrative of the present invention, and is not to beconstrued as limiting thereof. The invention is defined by the followingclaims, with equivalents of the claims to be included therein.

That which is claimed is:
 1. A pharmaceutical composition comprising anaptamer in a pharmaceutically acceptable carrier, wherein said aptamerselectively binds a cancer cell extracellular receptor protein, andwherein said aptamer is directly linked by covalent bonding to from 2 to10 toxin compounds.
 2. The composition of claim 1, wherein said covalentbonding comprises a geminal diamine linkage.
 3. The composition of claim2, wherein at least one of said toxin compounds is an anthracycline or ataxane having a free amine.
 4. The composition of claim 3, wherein saidaptamer is directly linked by covalent bonding to said anthracycline orsaid taxane at a CpG binding site on said aptamer.
 5. The composition ofclaim 1, wherein the half life of said covalent bonding to the toxincompounds is at least 5 hours in human blood plasma.
 6. The compositionof claim 1, wherein said aptamer comprises at least one FdUMP.
 7. Thecomposition of claim 1, wherein said aptamer is provided as a dimericcomplex.
 8. The composition of claim 7, wherein said cancer cellextracellular receptor protein is a dimeric protein and said dimericcomplex comprises a first nucleic acid that selectively binds to saidcancer cell extracellular receptor protein, a second nucleic acid thatalso selectively binds to said cancer cell extracellular receptorprotein, and a linker connecting said first and second nucleic acids. 9.The composition of claim 8, wherein said dimeric protein is prostatespecific membrane antigen (PSMA), transferrin receptor, carbonicanhydrase XII, or an ErbB receptor.
 10. The composition of claim 8,wherein said linker is double-stranded poly-DNA.
 11. The composition ofclaim 10, wherein said double-stranded poly-DNA comprises at least oneCpG binding site.
 12. The composition of claim 10, wherein saiddouble-stranded poly-DNA comprises a poly-T/poly-A region, wherein someor all of the poly-T residues are replaced by poly-FdU.
 13. A method ofselecting an aptamer that specifically binds to an extracellular surfaceprotein expressed by a cell of interest, wherein said aptamer comprisesat least one binding site for one or more active compounds, said methodcomprising the steps of: a. combining a first pool comprising differentnucleic acids with said extracellular surface protein or a fragmentthereof, wherein said nucleic acids comprise: i. a variable region from20 to 60 nucleotides long; and ii. primer regions flanking said variableregion and capable of binding a forward and reverse primer duringamplification, wherein each of said primer regions contains from 1 to 10mismatches with respect to said forward or reverse primer; and iii. oneor more binding sites for said active compounds; b. selecting a firstsubpopulation of nucleic acids from said first pool, said firstsubpopulation comprising at least one nucleic acid that specificallybinds to said extracellular surface protein; c. amplifying said at leastone nucleic acid of said first subpopulation, wherein said amplifying isperformed under conditions that allow priming at sites other than theprimer regions; and d. selecting a second subpopulation comprising atleast one nucleic acid species from said first subpopulation whichcomprises at least one binding site for one or more active compounds; tothereby select said aptamer.
 14. The method of claim 13, wherein saidaptamer has a shorter length than the nucleic acids of said first poolas a result of the priming at sites other than the primer regions. 15.The method of claim 13, wherein said binding sites for said activecompounds comprise a CpG site.
 16. The method of claim 13, wherein saidextracellular surface protein is expressed by a cancer cell.
 17. Themethod of claim 13, wherein said binding sites for said one or moreactive compounds comprise one or more CpG sites in said primer region.18. The method of claim 13, wherein said aptamer is capable of beinginternalized by said cell of interest
 19. The method of claim 13 furthercomprising the step of covalently binding said one or more activecompounds to said aptamer.
 20. The method of claim 19, wherein saidactive compounds comprise an anthracycline or a taxane.
 21. The methodof claim 20, wherein said anthracycline or said taxane is released bysaid aptamer at pH less than or equal to
 6. 22. The method of claim 21,wherein formaldehyde is produced when said anthracycline or said taxaneis released from said aptamer.